BtaINT0129445 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004770 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr19:48800776-48801622:-
Coord C1 exon
chr19:48801468-48801622
Coord A exon
chr19:48800950-48801467
Coord C2 exon
chr19:48800776-48800949
Length
518 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGC
5' ss Score
5.85
3' ss Seq
CCGCCTGCTGGTGCCCCCAGGCC
3' ss Score
8.72
Exon sequences
Seq C1 exon
CCTGCGTGCAGCGCTTTCCCTTCCTCTACGTGGACATCTCCCAGGGTCGAGGGAAGAAGTGGTGGACCCTCCGCAGGGCCTGCTTCAAGATCGTTGAGCACAACTGGTTTGAGACCTTCATTGTCTTCATGATCCTGCTCAGCAGTGGGGCCTTG
Seq A exon
GTAGGCGCCGCCCTGAGGGCCGGGCATGGGCAGGGGCAGGGGCCAGGCTGGAAGCAGGCTGTCCCAGGGCTCCCTCCTTTCTGCACCATGGGAGGAACACTTGCTGGACAGGCCCGAACCCAGAGAGAGAGCCCTGAAGAACTCACCAGTGCTTCCAGGGTGTGTGGCAGACTGTGCTCATTTTCACAAAGAGGCAGATGGGCTCTGACCCTGTGTGCCTCCCTGGCTGACAGGTCCCGACCAGGGAGCAGGTGGGAAGGGAATATGGGGTGGGGGGGCCAGCCTGTGTCACAGCAAACCCCCTGCAGGTTAGTGAACATTCCTATCATTAGGTCTGGGGAAGGGGAGCTGAGGGGCTTCCCCCCACCAGGAACTCCCCCGCTCACCCCCACGATGGGTGCGGGGAGTCTGCCCCCGCATCTAACCCCAGTGCCAGACCCCTGGGAACCAGCAGCTGTAGGGACATGGCTGCTGCCCCAGCCTCCGGGCCCTGGCCACCCGCCTGCTGGTGCCCCCAG
Seq C2 exon
GCCTTCGAGGACATCCACATTGAGCAGCGGCGAGTCATCCGCACCATCCTGGAGTACGCCGACAAGGTCTTCACCTACATCTTCATCCTGGAGATGCTACTCAAGTGGGTGGCCTACGGCTTCAAGGTGTACTTCACCAATGCCTGGTGCTGGCTCGACTTCCTCATCGTGGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004770:ENSBTAT00000006265:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=PD(19.2=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.1=67.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCGCTTTCCCTTCCTCTAC
R:
GTCCACGATGAGGAAGTCGAG
Band lengths:
321-839
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]